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Protein classification
The SCOPe (Structural Classification of Proteins — extended) database classifies proteins according to their overall shape. Unfortunately, the SCOPe database, which is maintained by the University of California - Berkeley, is scheduled to be shut down in the summer of 2017 due to lack of funding. This page attempts to categorize Foldit proteins according to the SCOPe classes. In sections below, puzzles shown on the same line involve proteins which should fold to a similar shape. This page is not being actively maintained as of February 2017. 3D images and distance maps for many proteins from these classes are shown at Distance Maps and http://memorize.com/protein-distance-maps. For complete lists of player-submitted images of puzzle results, see puzzle results - 379 to 1000 and puzzle results - 1001 and up. All alpha proteins - SCOPe Class a Mainly helices DNA/RNA-binding 3-helical bundle core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down Homeodomain-like Homeodomain Puzzle 476, Puzzle 481, Puzzle 696 Myb/SANT domain Puzzle 671, Puzzle 685, Puzzle 692 ARID-like Puzzle 698 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 3 helices; bundle, closed, right-handed twist; up-and-down: Puzzle 768 VHP, Villin headpiece domain 3 short helices; irregular array VHP VHP Chicken villin Histone-fold 3 helices; long middle helix is flanked at each end with shorter ones Histone Fold Nucleosome core histones form octamers composed of two copies of each of the four histones: Puzzle 761 4 helical up and down bundle 4 helices; bundle, closed or partly opened, left-handed twist; up-and-down Cytochromes Puzzle 711 Alpha-catenin/vinculin-like Puzzle 458 4-helical cytokines core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections: Puzzle 515, Puzzle 520, Symmetry_CASP_ROLL_R0007, Puzzle 554 Acyl carrier protein-like 4 helices, bundle; helix 3 is shorter than others; up-and-down Retrovirus capsid dimerization domain-like Puzzle 744 Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit 4 helices; bundle, closed, right-handed twist: Puzzle 672 EF Hand-like 4 helices; array of 2 hairpins, opened: Puzzle 754 PTS-regulatory domain, PRD core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection: Puzzle 512, Puzzle 634 All beta proteins - SCOPe Class b mainly sheets OB fold barrel, closed or partly opened n=5, S=10 or S=8; greek-key Nucleic acid-binding proteins Cold Shock BC4932-like Puzzle 451 Immunoglobulin-like beta-sandwich sandwich; 7 strands in 2 sheets; greek-key: Puzzle 452, Puzzle 462, Puzzle 432, Puzzle 437 Immunoglobulin Puzzle 550 V set domains (antibody variable domain-like) Puzzle 474 C1 set domains (antibody constant domain-like) Puzzle 477 Fibronectin type III Puzzle 491, Puzzle 505, Puzzle 507 PKD domain Puzzle 770 (close to 1BR4), Puzzle 788 Transglutaminase, two C-terminal domains Puzzle 461, Puzzle 464, Puzzle 482, Puzzle 485, Puzzle 542, Puzzle 546 ApaG-like Puzzle 408, Puzzle 433, Puzzle 435, Puzzle 442 E set domains Filamin repeat (rod domain) Puzzle 447, Puzzle 459, Puzzle 660 Invasin/intimin cell-adhesion fragments Puzzle 414, Puzzle 416, Puzzle 426, Puzzle 429, Puzzle 668 C2 domain-like sandwich; 8 strands in 2 sheets; greek-key PHL pollen allergen Puzzle 492, Puzzle 497 gamma-Crystallin-like Sandwich; 8 strands in 2 sheets; greek-key duplication: has internal pseudo twofold symmetry Puzzle 766 Supersandwich Puzzle 511, Puzzle 516, Puzzle 518 SH3-like barrel barrel, partly opened; n*=4, S*=8; meander the last strand is interrupted by a turn of 3-10 helix SH3-domain Puzzle 704 PDZ domain-like contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix: T-cell_Lymphoma Lipocalins barrel, closed or opened; n=8, S=12; meander Fatty acid binding protein-like ten-stranded meander beta-sheet folded upon itself, relates to the common fold by opening the barrel and insertion of beta-hairpin: Puzzle 733 WW domain-like core: 3-stranded meander beta-sheet WW domain Puzzle 415, Puzzle 420 Beta clip double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll AFP III-like domain duplication: consists of two structural repeats related by pseudo dyad Type III antifreeze protein, AFP III Puzzle 777 Alpha and beta proteins (a+b) - SCOPe Class d Mainly antiparallel beta sheets (segregated alpha and beta regions) Lysozyme-like common alpha+beta motif for the active site region Lysozyme-like C-type lysozyme Turkey_Egg_Lysozyme IL8-like beta(3)-alpha Interleukin 8-like chemokines Viral_Macrophage_Inflammatory_Protein DNA-binding domain beta(3)-alpha; 2 layers: alpha/beta: Puzzle 751 Dodecin subunit-like beta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132 Amyloid beta a4 protein copper binding domain (domain 2) Copper Ion Binding beta-Grasp (ubiquitin-like) core: beta(2)-alpha-beta(2); mixed beta-sheet 2143: Puzzle 784 2Fe-2S ferredoxin-like Puzzle 736 Cystatin-like alpha-beta(4); helix packs against coiled antiparallel beta-sheet: Puzzle 611 Cystatin/monellin Puzzle 573, Puzzle 580 Cystatins Potato_Multicystatin dsRBD-like alpha-beta(3)-alpha; 2 layers: alpha/beta: Puzzle 728, Puzzle 730, Puzzle 732 Alpha-lytic protease prodomain-like core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta Fe-S cluster assembly (FSCA) domain-like NifU C-terminal domain-like Puzzle 693, Puzzle 699 GroEL-intermediate domain like 3-helical bundle packed against 3-stranded mixed beta-sheet: Puzzle 535, Puzzle 544, Puzzle 547 Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2 HMA, heavy metal-associated domain Puzzle 785 Killer toxin KP6 alpha-subunit Killer Toxin RNA-binding domain, RBD beta(3)-alpha; 2 layers: alpha/beta Canonical RBD Puzzle 417, Puzzle 431 Acylphosphatase/BLUF domain-like Acylphosphatase-like Puzzle 506 Probable bacterial effector-binding domain duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12) Probable bacterial effector-binding domain Gyrase inhibitory protein Gyr Puzzle 438, Puzzle 446, Puzzle 473, Puzzle 498 Secretion chaperone-like alpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/beta Type III secretory system chaperone-like Type III secretory system chaperone Puzzle 456, Puzzle 472 beta-Grasp (ubiquitin-like) core: beta(2)-alpha-beta(2); mixed beta-sheet 2143: Puzzle 469 Immunoglobulin-binding domains Streptococcal_Protein Pili subunits contains very long N-terminal helix, which end is packed against beta-sheet Pili subunits Puzzle 470 Profilin-like 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha PYP-like sensor domain (PAS domain) alpha-beta(2)-alpha(2)-beta(3): Puzzle 517, Puzzle 521, Puzzle 524 GYF/BRK domain-like beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta GYF domain Puzzle 729 TBP-like Puzzle 411 Bet v1-like Puzzle 613 Protein kinase-like (PK-like) Puzzle 478 gpW/XkdW-like alpha-beta(2)-alpha; antiparallel hairpin: Puzzle 500 SufE/NifU alpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123: Puzzle 551 Alpha and beta proteins (a/b) - SCOPe Class c Mainly parallel beta sheets (beta-alpha-beta units) The "swivelling" beta/beta/alpha domain 3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology GroEL apical domain like GroEL-like chaperone, apical domain Puzzle 412 Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) 2 curved layers, a/b; parallel beta-sheet; order 1234...N: Puzzle 527, Puzzle 534 Flavodoxin-like 3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345 CheY-like Puzzle 434, Puzzle 436, Puzzle 440, Puzzle 445, Puzzle 449, Puzzle 453, Puzzle 454, Puzzle 488, Puzzle 502 CheY-related Puzzle 483 SGNH hydrolase Puzzle 584, Puzzle 588 Phosphotyrosine protein phosphatases I-like 3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134 PTS system IIB component-like Puzzle 658, Puzzle 700 Thioredoxin fold core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest Thioredoxin-like core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest: Puzzle 621 Thioltransferase Puzzle 455, Puzzle 622, Puzzle 467, Puzzle 739, Puzzle 746 Txnl5-like Puzzle 457, Puzzle 463, Puzzle 480, Puzzle 486 Nucleotide-diphospho-sugar transferases Puzzle 618 Membrane and cell surface proteins and peptides - SCOPe Class f Family A G protein-coupled receptor-like core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane: Puzzle 726 Small proteins - SCOPe Class g Insulin-like nearly all-alpha can be classified as disulfide-rich: Puzzle 707 Knottins (small inhibitors, toxins, lectins) disulfide-bound fold; contains beta-hairpin with two adjacent disulfides Scorpion toxin-like Short-chain scorpion toxins Scorpion_Toxin, Puzzle 762 Defensin-like Disulfide-rich fold, nearly all-beta Defensin-like Puzzle 548, Puzzle 624, Platypus Venom, Puzzle 774 Crambin-like disulfide-rich alpha+beta fold: Puzzle 781, Puzzle 790 FYVE/PHD zinc finger Puzzle 615 Coiled coil proteins - SCOPe Class h Parallel coiled-coil Coiled-coil dimerization domain from cortexillin I Puzzle 479 Category:Puzzle Results